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https://www.readbyqxmd.com/read/28734034/protein-features-as-determinants-of-wild-type-glycoside-hydrolase-thermostability
#1
Henrik Marcus Geertz-Hansen, Lars Kiemer, Morten Nielsen, Kiril Stanchev, Nikolaj Blom, Søren Brunak, Thomas Nordahl Petersen
Thermostable enzymes for conversion of lignocellulosic biomass into biofuels have significant advantages over enzymes with more moderate themostability due to the challenging application conditions. Experimental discovery of thermostable enzymes is highly cost intensive, and the development of in-silico methods guiding the discovery process would be of high value. To develop such an in-silico method and provide the data foundation of it, we determined the melting temperatures of 602 fungal glycoside hydrolases from the families GH5, 6, 7, 10, 11, 43 and AA9 (formerly GH61)...
July 22, 2017: Proteins
https://www.readbyqxmd.com/read/28733938/molecular-cloning-heterologous-expression-and-functional-characterization-of-a-cellulolytic-enzyme-cel-prii-from-buffalo-rumen-metagenome
#2
Ravi K Shah, Amrutlal K Patel, Deepti M Davla, Ishan K Parikh, Ramalingam B Subramanian, Kamlesh C Patel, Subhash J Jakhesara, Chaitanya G Joshi
A cellulase encoding gene, Cel PRII, was identified from Mehsani buffalo rumen metagenome, and cloned and expressed in Escherichia coli BL21(DE3)pLysS. The 1170 bp full length gene encodes a 389 residue polypeptide (Cel PRII) containing a catalytic domain belonging to glycosyl hydrolase (GH) 5 family. The fusion protein consisting of the Cel PRII, thioredoxin tag and 6x Histidine tag with predicted molecular weight of 63 kDa when recovered from inclusion bodies under denaturing conditions, exhibited cellulolytic activity against carboxymethyl cellulose (CMC)...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28731682/cold-adaptation-of-triosephosphate-isomerase
#3
Johan Åqvist
The main problem for enzymes from psychrophilic species, that need to work near the freezing point of liquid water, is the exponential decay of reaction rates as the temperature is lowered. Cold-adapted enzymes have solved this problem by shifting the activation enthalpy-entropy balance for the catalyzed reaction compared to their mesophilic orthologs. To understand the structural basis of this universal feature it is necessary to examine pairs of such orthologous enzymes, with known 3D structures, at the microscopic level...
July 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#4
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28728936/cell-free-pipeline-for-discovery-of-thermotolerant-xylanases-and-endo-1-4-%C3%AE-glucanases
#5
Dejan Gagoski, Zhenyu Shi, Lars Keld Nielsen, Claudia E Vickers, Stephen Mahler, Robert Speight, Wayne A Johnston, Kirill Alexandrov
The rapid expansion in the number of sequenced genomes and metagenomes provides an exceptional resource for mining of the enzymes with biotechnologically relevant properties. However, the majority of protein production and analysis methods are not sufficiently cost-efficient and scalable to experimentally verify the results of computational genomic mining. Here, we present a pipeline based on Leishmania tarentolae cell-free system that was used to characterise 30 putative thermostable endo-1,4-β-glucanases and xylanases identified in public genomic databases...
July 17, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28728005/thermal-destruction-of-organic-waste-hydrophobicity-for-agricultural-soils-application
#6
Francisco Comino, Víctor Aranda, Ana Domínguez-Vidal, María José Ayora-Cañada
Use of organic amendments is a good strategy for combating the growing problem of soil degradation due to deterioration of organic matter content, particularly severe in semi-arid European Mediterranean regions, while at the same time providing an opportunity for recycling organic wastes. Olive mill pomace (OMP), the main by-product of the olive oil industry, is being used increasingly in olive grove soils for this purpose. Although the positive effects of OMP amendments have been widely studied, they also have some negative effects on soil...
July 17, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28723955/crystal-structure-and-functional-characterization-of-an-isoaspartyl-dipeptidase-cpsiada-from-colwellia-psychrerythraea-strain-34h
#7
Sun-Ha Park, Chang Woo Lee, Sung Gu Lee, Seung Chul Shin, Hak Jun Kim, Hyun Park, Jun Hyuck Lee
Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site...
2017: PloS One
https://www.readbyqxmd.com/read/28722353/auramine-o-an-incense-smoke-ingredient-promotes-lung-cancer-malignancy
#8
Jia-Chen Tung, Wei-Chien Huang, Juan-Cheng Yang, Guan-Yu Chen, Chi-Chen Fan, Yu-Chuan Chien, Pei-Shan Lin, Shih-Chun Candice Lung, Wei-Chao Chang
Burning incense to worship deities is a popular religious ritual in large parts of Asia, and is a popular custom affecting more than 1.5 billion adherents. Due to incomplete combustion, burning incense has been well recognized to generate airborne hazards to human health. However, the correlation between burning incense and lung cancer in epidemiological studies remains controversy. Therefore, we speculated that some unknown materials in incense smoke are involved in the initiation or progression of lung cancer...
July 19, 2017: Environmental Toxicology
https://www.readbyqxmd.com/read/28722269/role-of-q177a-and-k173a-q177a-substitutions-in-thermostability-and-activity-of-the-elbn12-lipase
#9
Parisa Farrokh, Bagher Yakhchali, Ali Asghar Karkhane
Thermostable lipases have many applications in detergent industries and in organic synthesis. There are many ways to improve thermal stability of enzymes e.g., higher hydrophobicity, greater structural packing, higher content of the charged residues and lower thermolabile ones. In this study, thermolabile Gln (sensitive to higher temperatures) was substituted with Ala in native ELBn12 and mutated K173A lipases 2, to examine its effect on thermal stability and activity of the lipases. Single (Q177A) and double mutants (K173A/Q177A) were expressed in Escherichia coli pLysS...
July 19, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28722241/mineralized-state-of-the-avian-influenza-virus-in-the-environment
#10
Hangyu Zhou, Guangchuan Wang, Xiaoyu Wang, Zhiyong Song, Ruikang Tang
Although the circulation of avian influenza in humans is limited, they can be transmitted from Aves to humans, representing a great challenge. Herein, we suggest that influenza viruses from Aves might exist in a mineralized state due to the high calcium concentrations in the avian intestine. Using two typical influenza viruses as examples, we demonstrate these viruses can self-mineralize in simulated avian intestinal fluid, resulting in egg-like virus-mineral structured composites. The mineralized viruses are more robust, with enhanced infectivity and thermostability...
July 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28720851/microneedle-patch-delivery-of-influenza-vaccine-during-pregnancy-enhances-maternal-immune-responses-promoting-survival-and-long-lasting-passive-immunity-to-offspring
#11
E Stein Esser, Joanna A Pulit-Penaloza, Haripriya Kalluri, Devin McAllister, Elena V Vassilieva, Elizabeth Q Littauer, Nadia Lelutiu, Mark R Prausnitz, Richard W Compans, Ioanna Skountzou
Influenza virus causes life-threatening infections in pregnant women and their newborns. Immunization during pregnancy is the most effective means of preventing maternal and infant mortality/morbidity; however, influenza vaccination rates of pregnant women remain under 50%. Furthermore, the availability of vaccines in low-resource populations is limited. Skin immunization with microneedle patches (MN) is a novel and safe vaccination platform featuring thermostable vaccine formulations. Cold-chain independence and the potential for self-administration can expand influenza vaccination coverage in developing countries...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28719655/protein-analysis-and-gene-expression-indicate-differential-vulnerability-of-iberian-fish-species-under-a-climate-change-scenario
#12
Tiago F Jesus, João M Moreno, Tiago Repolho, Alekos Athanasiadis, Rui Rosa, Vera M F Almeida-Val, Maria M Coelho
Current knowledge on the biological responses of freshwater fish under projected scenarios of climate change remains limited. Here, we examine differences in the protein configuration of two endemic Iberian freshwater fish species, Squalius carolitertii and the critically endangered S. torgalensis that inhabit in the Atlantic-type northern and in the Mediterranean-type southwestern regions, respectively. We performed protein structure modeling of fourteen genes linked to protein folding, energy metabolism, circadian rhythms and immune responses...
2017: PloS One
https://www.readbyqxmd.com/read/28715205/polymerase-chain-transcription-exponential-synthesis-of-rna-and-modified-rna
#13
Tingjian Chen, Floyd E Romesberg
There is increasing demand for RNA and modified RNA oligonucleotides, but in contrast to DNA oligonucleotides, they are typically prohibitively expensive to chemically synthesize, and unlike longer RNAs, they are only inefficiently produced by in vitro transcription, especially when modified. To address these challenges, we previously reported the evolution of a thermostable DNA polymerase, SFM4-3, that more efficiently accepts substrates with 2'-substituents. We now show that SFM4-3 efficiently transcribes RNA or 2'-F-modified RNA and that it also efficiently PCR amplifies oligonucleotides of mixed RNA and DNA composition...
July 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28711560/interaction-of-carbapenems-and-%C3%AE-lactamase-inhibitors-towards-ctx-m-15-and-ctx-m-15-g238c-mutant
#14
Alessia Sabatini, Fabrizia Brisdelli, Giuseppe Celenza, Francesca Marcoccia, Martina Colapietro, María M Tavío, Alessandra Piccirilli, Gianfranco Amicosante, Mariagrazia Perilli
OBJECTIVES: The aim of this study was to evaluate the role of residue 238 in CTX-M-15 and CTX-M-15(G238C) mutant with respect to carbapenems and various β-lactamase inhibitors. METHODS: A CTX-M-15(G238C) laboratory mutant was generated by site-directed mutagenesis from CTX-M-15 enzyme by replacing glycine 238 with cysteine. Thiol titration and p-chloromercuribenzoate (PCMB) inactivation assays were used to ascertain the presence of a disulfide bridge in the active site of CTX-M-15(G238C)...
July 12, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28710637/stabilization-of-enzymes-by-using-thermophiles
#15
Ana Luisa Ribeiro, Mercedes Sánchez, Aurelio Hidalgo, José Berenguer
Manufactured steroid compounds have many applications in the pharmaceutical industry. Due to the chemical complexity and chirality of steroids, there is an increasing demand for enzyme-based bioconversion processes to replace those based on chemical synthesis. In this context, thermostability of the involved enzymes is a highly desirable property as both the increased half-life of the enzyme and the enhanced solubility of substrates and products will improve the yield of the reactions. Metagenomic libraries from thermal environments are potential sources of thermostable enzymes of prokaryotic origin, but the number of expected hits could be quite low for enzymes handling substrates such as steroids, rarely found in prokaryotes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28710270/stabilization-of-multimeric-proteins-via-inter-subunits-cyclization
#16
Lu Zhu, Shuwen Wang, Wenya Tian, Yeqi Zhang, Yang Song, Jun Zhang, Bo Mu, Chao Peng, Zixin Deng, Hongmin Ma, Xudong Qu
Proteins with high catalytic efficiency and selectivity under mild conditions have long been appreciated by industrial and medicinal fields. These proteins, which are commonly multimeric, often possess low stability impeding wider application. Currently, strategies to improve the stability of multimeric proteins concentrate on enhancing the interaction at internal-interface of the subunits. In this report, we confirmed that the largely underestimated subunit terminal ends are as significant as the internal-interface for protein stability...
July 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28709882/biodegradation-of-food-waste-using-microbial-cultures-producing-thermostable-%C3%AE-amylase-and-cellulase-under-different-ph-and-temperature
#17
Mukesh Kumar Awasthi, Jonathan W C Wong, Sunil Kumar, Sanjeev Kumar Awasthi, Quan Wang, Meijing Wang, Xiuna Ren, Junchao Zhao, Hongyu Chen, Zengqiang Zhang
The aim of this work was to study the biodegradation of food waste employing thermostable α-amylase and cellulase enzymes producing bacteria. Four potential isolates were identified which were capable of producing maximum amylase and cellulase and belong to the amylolytic strains, Brevibacillus borstelensis and Bacillus licheniformis; cellulolytic strains, Bacillus thuringiensis and Bacillus licheniformis, respectively. These strains were selected based on its higher cell density, enzymatic activities and stability at a wide range of pH and temperature compared to other strains...
June 30, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28709846/biocatalysis-for-the-synthesis-of-pharmaceuticals-and-pharmaceutical-intermediates
#18
REVIEW
Huihua Sun, Hongfang Zhang, Ee Lui Ang, Huimin Zhao
Biocatalysis has been increasingly used for pharmaceutical synthesis in an effort to make manufacturing processes greener and more sustainable. Biocatalysts that possess excellent activity, specificity, thermostability and solvent-tolerance are highly sought after to meet the requirements of practical applications. Generating biocatalysts with these specific properties can be achieved by either discovery of novel biocatalysts or protein engineering. Meanwhile, chemoenzymatic routes have also been designed and developed for pharmaceutical synthesis on an industrial scale...
June 28, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28707884/rapid-and-programmable-protein-mutagenesis-using-plasmid-recombineering
#19
Sean Andrew Higgins, Sorel Ounkap, David F Savage
Comprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. However, current techniques enabling comprehensive protein mutagenesis are based on PCR and require in vitro reactions involving specialized protocols and reagents. This has complicated efforts to rapidly and reliably produce desired comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space...
July 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28703279/lactulose-production-by-a-thermostable-glycoside-hydrolase-from-the-hyperthermophilic-archaeon-caldivirga-maquilingensis-ic-167
#20
Rebaone Letsididi, Hinawi A M Hassanin, Marwa Y F Koko, Tao Zhang, Bo Jiang, Wanmeng Mu
BACKGROUND: Lactulose has various uses in the food and pharmaceutical fields. Thermostable enzymes have many advantages for industrial exploitation, including high substrate solubilities as well as reduced risk of process contamination. RESULTS: Enzymatic synthesis of lactulose employing a transgalactosylation reaction by a recombinant thermostable GH1 from the hyperthermophilic archaeon Caldivirga maquilingensis IC-167 was investigated and its optimum pH for lactulose production was found to be 4...
July 12, 2017: Journal of the Science of Food and Agriculture
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